Starting phenix.real_space_refine on Sun Mar 10 14:42:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/03_2024/8c92_16499.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/03_2024/8c92_16499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/03_2024/8c92_16499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/03_2024/8c92_16499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/03_2024/8c92_16499.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c92_16499/03_2024/8c92_16499.pdb" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1873 5.49 5 S 37 5.16 5 C 26245 2.51 5 N 9999 2.21 5 O 15335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 53489 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 40250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1873, 40250 Classifications: {'RNA': 1873} Modifications used: {'rna2p_pur': 171, 'rna2p_pyr': 98, 'rna3p_pur': 927, 'rna3p_pyr': 677} Link IDs: {'rna2p': 269, 'rna3p': 1603} Chain breaks: 6 Chain: "D" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1306 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain breaks: 1 Chain: "E" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1438 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain breaks: 1 Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 778 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain breaks: 1 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 789 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "2" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 312 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "Z" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 439 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Time building chain proxies: 22.91, per 1000 atoms: 0.43 Number of scatterers: 53489 At special positions: 0 Unit cell: (151.25, 205, 203.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 1873 15.00 O 15335 8.00 N 9999 7.00 C 26245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 24.13 Conformation dependent library (CDL) restraints added in 2.1 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3126 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 22 sheets defined 34.4% alpha, 18.1% beta 618 base pairs and 876 stacking pairs defined. Time for finding SS restraints: 18.96 Creating SS restraints... Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 61 through 71 removed outlier: 3.837A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 removed outlier: 4.098A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.596A pdb=" N ILE E 175 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 removed outlier: 4.251A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 11 removed outlier: 4.021A pdb=" N VAL J 11 " --> pdb=" O PRO J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 96 through 109 removed outlier: 4.044A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.729A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 113 removed outlier: 3.927A pdb=" N MET K 113 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 33 removed outlier: 3.902A pdb=" N GLY L 31 " --> pdb=" O GLY L 28 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY L 32 " --> pdb=" O LYS L 29 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG L 33 " --> pdb=" O THR L 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 33' Processing helix chain 'L' and resid 70 through 74 removed outlier: 3.534A pdb=" N ILE L 73 " --> pdb=" O LYS L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 138 removed outlier: 3.623A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.741A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.985A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 72 through 79 Processing helix chain 'N' and resid 82 through 87 Processing helix chain 'P' and resid 2 through 10 Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 removed outlier: 3.550A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 19 removed outlier: 3.732A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 72 removed outlier: 4.094A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.900A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 117 removed outlier: 4.256A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 23 removed outlier: 4.029A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.693A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 4.225A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 8 Processing helix chain 'T' and resid 17 through 27 removed outlier: 4.103A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 52 Processing helix chain 'U' and resid 65 through 67 No H-bonds generated for 'chain 'U' and resid 65 through 67' Processing helix chain 'Y' and resid 2 through 8 removed outlier: 4.085A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 33 removed outlier: 3.728A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN Y 31 " --> pdb=" O ASN Y 27 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 56 removed outlier: 4.265A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 Processing helix chain '0' and resid 17 through 20 removed outlier: 4.049A pdb=" N ALA 0 20 " --> pdb=" O SER 0 17 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 17 through 20' Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 24 removed outlier: 3.950A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 removed outlier: 3.747A pdb=" N ARG 2 28 " --> pdb=" O THR 2 24 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN 2 29 " --> pdb=" O LYS 2 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing sheet with id=AA1, first strand: chain 'D' and resid 169 through 175 removed outlier: 5.124A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 33 through 38 removed outlier: 5.422A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE D 48 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE D 82 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 116 through 119 removed outlier: 4.115A pdb=" N MET D 165 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N PHE D 118 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY D 163 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 120 removed outlier: 7.075A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.163A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN J 138 " --> pdb=" O TRP J 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 73 through 75 Processing sheet with id=AA7, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.597A pdb=" N VAL K 19 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE K 41 " --> pdb=" O LEU K 58 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU K 58 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.893A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 122 through 123 removed outlier: 5.486A pdb=" N VAL L 122 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'N' and resid 33 through 37 removed outlier: 6.101A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.714A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 19 through 22 removed outlier: 7.330A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 72 through 77 Processing sheet with id=AB5, first strand: chain 'S' and resid 2 through 10 removed outlier: 5.846A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 82 through 84 Processing sheet with id=AB7, first strand: chain 'T' and resid 11 through 14 removed outlier: 3.958A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR T 86 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 33 through 35 removed outlier: 7.027A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 40 through 44 removed outlier: 3.985A pdb=" N VAL U 41 " --> pdb=" O LYS U 60 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS U 60 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 82 through 84 Processing sheet with id=AC2, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AC3, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AC4, first strand: chain 'Z' and resid 35 through 37 removed outlier: 3.885A pdb=" N VAL Z 35 " --> pdb=" O ILE Z 6 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE Z 6 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG Z 37 " --> pdb=" O ILE Z 4 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE Z 4 " --> pdb=" O ARG Z 37 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1571 hydrogen bonds 2526 hydrogen bond angles 0 basepair planarities 618 basepair parallelities 876 stacking parallelities Total time for adding SS restraints: 48.62 Time building geometry restraints manager: 25.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9943 1.34 - 1.46: 24957 1.46 - 1.58: 19762 1.58 - 1.70: 3739 1.70 - 1.82: 71 Bond restraints: 58472 Sorted by residual: bond pdb=" C1' U A 827 " pdb=" N1 U A 827 " ideal model delta sigma weight residual 1.480 1.572 -0.092 1.50e-02 4.44e+03 3.75e+01 bond pdb=" N MET R 1 " pdb=" CA MET R 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" N ALA 0 1 " pdb=" CA ALA 0 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N ALA U 1 " pdb=" CA ALA U 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 ... (remaining 58467 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.23: 11374 107.23 - 113.91: 36765 113.91 - 120.59: 21023 120.59 - 127.26: 14958 127.26 - 133.94: 4141 Bond angle restraints: 88261 Sorted by residual: angle pdb=" N ALA T 13 " pdb=" CA ALA T 13 " pdb=" C ALA T 13 " ideal model delta sigma weight residual 108.13 112.39 -4.26 9.00e-01 1.23e+00 2.24e+01 angle pdb=" N VAL K 63 " pdb=" CA VAL K 63 " pdb=" C VAL K 63 " ideal model delta sigma weight residual 111.81 108.98 2.83 8.60e-01 1.35e+00 1.08e+01 angle pdb=" N LEU Y 57 " pdb=" CA LEU Y 57 " pdb=" CB LEU Y 57 " ideal model delta sigma weight residual 114.17 110.71 3.46 1.14e+00 7.69e-01 9.20e+00 angle pdb=" CB MET R 1 " pdb=" CG MET R 1 " pdb=" SD MET R 1 " ideal model delta sigma weight residual 112.70 120.63 -7.93 3.00e+00 1.11e-01 6.99e+00 angle pdb=" CG MET N 110 " pdb=" SD MET N 110 " pdb=" CE MET N 110 " ideal model delta sigma weight residual 100.90 106.23 -5.33 2.20e+00 2.07e-01 5.87e+00 ... (remaining 88256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 32888 35.87 - 71.73: 4030 71.73 - 107.60: 487 107.60 - 143.46: 17 143.46 - 179.33: 5 Dihedral angle restraints: 37427 sinusoidal: 32595 harmonic: 4832 Sorted by residual: dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual 232.00 52.67 179.33 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A 828 " pdb=" C1' U A 828 " pdb=" N1 U A 828 " pdb=" C2 U A 828 " ideal model delta sinusoidal sigma weight residual -128.00 44.49 -172.49 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C A 323 " pdb=" C1' C A 323 " pdb=" N1 C A 323 " pdb=" C2 C A 323 " ideal model delta sinusoidal sigma weight residual -128.00 10.78 -138.78 1 1.70e+01 3.46e-03 5.82e+01 ... (remaining 37424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 8578 0.029 - 0.057: 2471 0.057 - 0.086: 180 0.086 - 0.114: 153 0.114 - 0.143: 45 Chirality restraints: 11427 Sorted by residual: chirality pdb=" C1' U A 827 " pdb=" O4' U A 827 " pdb=" C2' U A 827 " pdb=" N1 U A 827 " both_signs ideal model delta sigma weight residual False 2.47 2.61 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" C1' G A1343 " pdb=" O4' G A1343 " pdb=" C2' G A1343 " pdb=" N9 G A1343 " both_signs ideal model delta sigma weight residual False 2.46 2.32 0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" C3' A A1420 " pdb=" C4' A A1420 " pdb=" O3' A A1420 " pdb=" C2' A A1420 " both_signs ideal model delta sigma weight residual False -2.74 -2.61 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 11424 not shown) Planarity restraints: 4167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 269 " 0.004 2.00e-02 2.50e+03 1.53e-02 5.28e+00 pdb=" N1 C A 269 " -0.005 2.00e-02 2.50e+03 pdb=" C2 C A 269 " 0.035 2.00e-02 2.50e+03 pdb=" O2 C A 269 " -0.025 2.00e-02 2.50e+03 pdb=" N3 C A 269 " 0.000 2.00e-02 2.50e+03 pdb=" C4 C A 269 " 0.012 2.00e-02 2.50e+03 pdb=" N4 C A 269 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C A 269 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A 269 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 468 " 0.017 2.00e-02 2.50e+03 1.32e-02 5.26e+00 pdb=" N9 G A 468 " -0.006 2.00e-02 2.50e+03 pdb=" C8 G A 468 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A 468 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G A 468 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G A 468 " -0.024 2.00e-02 2.50e+03 pdb=" O6 G A 468 " 0.020 2.00e-02 2.50e+03 pdb=" N1 G A 468 " 0.020 2.00e-02 2.50e+03 pdb=" C2 G A 468 " -0.019 2.00e-02 2.50e+03 pdb=" N2 G A 468 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A 468 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G A 468 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1333 " 0.006 2.00e-02 2.50e+03 1.30e-02 5.07e+00 pdb=" N9 G A1333 " -0.003 2.00e-02 2.50e+03 pdb=" C8 G A1333 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A1333 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A1333 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A1333 " -0.014 2.00e-02 2.50e+03 pdb=" O6 G A1333 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G A1333 " 0.007 2.00e-02 2.50e+03 pdb=" C2 G A1333 " -0.034 2.00e-02 2.50e+03 pdb=" N2 G A1333 " 0.021 2.00e-02 2.50e+03 pdb=" N3 G A1333 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G A1333 " 0.002 2.00e-02 2.50e+03 ... (remaining 4164 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 326 2.48 - 3.08: 34967 3.08 - 3.69: 102271 3.69 - 4.29: 141937 4.29 - 4.90: 195261 Nonbonded interactions: 474762 Sorted by model distance: nonbonded pdb=" O2' G A 214 " pdb=" O4' G A 215 " model vdw 1.872 2.440 nonbonded pdb=" OP2 G A1521 " pdb=" O2' A A1522 " model vdw 1.916 2.440 nonbonded pdb=" OP2 G A 989 " pdb=" OG SER Z 11 " model vdw 1.942 2.440 nonbonded pdb=" O2' G A1666 " pdb=" O4' G A1667 " model vdw 1.966 2.440 nonbonded pdb=" O3' C A2730 " pdb=" OG SER D 174 " model vdw 1.973 2.440 ... (remaining 474757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 7.560 Check model and map are aligned: 0.610 Set scattering table: 0.390 Process input model: 153.690 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.092 58472 Z= 0.096 Angle : 0.377 7.931 88261 Z= 0.197 Chirality : 0.026 0.143 11427 Planarity : 0.002 0.034 4167 Dihedral : 22.722 179.329 34301 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1660 helix: 1.69 (0.25), residues: 515 sheet: 0.50 (0.32), residues: 248 loop : -0.58 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 30 HIS 0.006 0.001 HIS R 82 PHE 0.006 0.001 PHE S 75 TYR 0.011 0.001 TYR N 112 ARG 0.004 0.000 ARG Z 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 GLN cc_start: 0.8247 (mt0) cc_final: 0.7959 (mm110) REVERT: J 53 TYR cc_start: 0.7762 (m-80) cc_final: 0.7514 (m-80) REVERT: J 138 GLN cc_start: 0.7246 (mp10) cc_final: 0.6871 (mp10) REVERT: K 41 ILE cc_start: 0.8491 (pt) cc_final: 0.8274 (tt) REVERT: K 75 SER cc_start: 0.8237 (m) cc_final: 0.7666 (p) REVERT: L 126 ARG cc_start: 0.1247 (mtm180) cc_final: 0.0636 (ttp80) REVERT: N 35 LYS cc_start: 0.8806 (tttm) cc_final: 0.8363 (ttpp) REVERT: S 12 SER cc_start: 0.9087 (p) cc_final: 0.8879 (p) REVERT: S 110 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7828 (tpp-160) REVERT: 0 11 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8505 (mtmm) REVERT: 2 12 ARG cc_start: 0.8698 (tpp80) cc_final: 0.8158 (tpp-160) REVERT: 2 16 HIS cc_start: 0.7332 (m-70) cc_final: 0.7085 (m170) REVERT: Z 22 THR cc_start: 0.8876 (m) cc_final: 0.8640 (p) REVERT: Z 37 ARG cc_start: 0.6751 (mmt-90) cc_final: 0.6439 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.5132 time to fit residues: 270.2521 Evaluate side-chains 213 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 204 optimal weight: 0.2980 chunk 317 optimal weight: 0.8980 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 5 GLN ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN S 57 ASN ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 ASN 0 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 58472 Z= 0.247 Angle : 0.545 9.761 88261 Z= 0.272 Chirality : 0.029 0.189 11427 Planarity : 0.004 0.041 4167 Dihedral : 23.284 179.549 30992 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.02 % Favored : 93.92 % Rotamer: Outliers : 2.45 % Allowed : 10.66 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1660 helix: 0.95 (0.24), residues: 512 sheet: 0.26 (0.30), residues: 277 loop : -0.64 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 78 HIS 0.010 0.001 HIS R 82 PHE 0.011 0.002 PHE N 80 TYR 0.012 0.002 TYR Q 46 ARG 0.007 0.001 ARG Y 7 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 234 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 138 GLN cc_start: 0.7695 (mp10) cc_final: 0.7214 (mp10) REVERT: L 126 ARG cc_start: 0.1793 (mtm180) cc_final: 0.0903 (ttp80) REVERT: N 106 ASP cc_start: 0.7859 (t0) cc_final: 0.7569 (t0) REVERT: R 31 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8051 (mm-30) REVERT: S 110 ARG cc_start: 0.8253 (tpp-160) cc_final: 0.7938 (tpp-160) REVERT: T 79 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8055 (p0) REVERT: 2 16 HIS cc_start: 0.7876 (m-70) cc_final: 0.7619 (m170) outliers start: 34 outliers final: 24 residues processed: 250 average time/residue: 0.5132 time to fit residues: 217.6620 Evaluate side-chains 233 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 207 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 2 residue 26 ASN Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 318 optimal weight: 5.9990 chunk 343 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 chunk 315 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 255 optimal weight: 30.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 HIS ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 58472 Z= 0.215 Angle : 0.516 8.939 88261 Z= 0.262 Chirality : 0.030 0.237 11427 Planarity : 0.004 0.041 4167 Dihedral : 23.348 178.624 30992 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.17 % Allowed : 13.98 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1660 helix: 0.46 (0.23), residues: 518 sheet: 0.19 (0.31), residues: 278 loop : -0.81 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 78 HIS 0.010 0.001 HIS R 82 PHE 0.011 0.001 PHE N 80 TYR 0.013 0.002 TYR J 75 ARG 0.006 0.001 ARG K 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 230 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 TRP cc_start: 0.8528 (m100) cc_final: 0.7672 (m100) REVERT: E 100 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8278 (ttm) REVERT: J 138 GLN cc_start: 0.7663 (mp10) cc_final: 0.7116 (mp10) REVERT: K 113 MET cc_start: 0.8030 (mmt) cc_final: 0.7639 (mmt) REVERT: L 18 ARG cc_start: 0.7483 (mtp180) cc_final: 0.6759 (mtm180) REVERT: L 126 ARG cc_start: 0.1714 (mtm180) cc_final: 0.0579 (ttp80) REVERT: R 37 GLU cc_start: 0.8325 (pm20) cc_final: 0.7845 (pm20) REVERT: S 110 ARG cc_start: 0.8232 (tpp-160) cc_final: 0.7922 (tpp-160) REVERT: T 79 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8063 (p0) REVERT: 0 11 LYS cc_start: 0.9083 (tppp) cc_final: 0.8674 (tppt) REVERT: 2 12 ARG cc_start: 0.8638 (tpp80) cc_final: 0.8140 (tpp-160) REVERT: 2 16 HIS cc_start: 0.8014 (m-70) cc_final: 0.7661 (m170) outliers start: 44 outliers final: 30 residues processed: 254 average time/residue: 0.5397 time to fit residues: 231.7875 Evaluate side-chains 240 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 208 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain Z residue 50 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 8.9990 chunk 239 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 151 optimal weight: 30.0000 chunk 213 optimal weight: 10.0000 chunk 319 optimal weight: 0.0060 chunk 338 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 overall best weight: 7.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 16 HIS Z 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 58472 Z= 0.358 Angle : 0.698 12.364 88261 Z= 0.351 Chirality : 0.037 0.246 11427 Planarity : 0.005 0.090 4167 Dihedral : 23.776 177.500 30992 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.01 % Favored : 91.93 % Rotamer: Outliers : 4.76 % Allowed : 14.70 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.20), residues: 1660 helix: -0.05 (0.22), residues: 509 sheet: -0.31 (0.31), residues: 271 loop : -1.12 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP T 80 HIS 0.015 0.002 HIS R 82 PHE 0.025 0.002 PHE Y 26 TYR 0.013 0.002 TYR D 45 ARG 0.018 0.001 ARG T 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 217 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 78 TRP cc_start: 0.8741 (m100) cc_final: 0.7903 (m100) REVERT: K 113 MET cc_start: 0.8304 (mmt) cc_final: 0.8064 (mmt) REVERT: N 110 MET cc_start: 0.7432 (ttt) cc_final: 0.7159 (ttt) REVERT: R 34 GLU cc_start: 0.8933 (tt0) cc_final: 0.8716 (tt0) REVERT: S 110 ARG cc_start: 0.8360 (tpp-160) cc_final: 0.8042 (tpp-160) REVERT: T 79 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.7968 (p0) REVERT: 0 3 GLN cc_start: 0.6675 (OUTLIER) cc_final: 0.6138 (pt0) REVERT: 2 12 ARG cc_start: 0.8849 (tpp80) cc_final: 0.8496 (tpp-160) REVERT: 2 16 HIS cc_start: 0.8343 (m90) cc_final: 0.8126 (m90) REVERT: 2 28 ARG cc_start: 0.8691 (mtt90) cc_final: 0.8249 (mtt90) outliers start: 66 outliers final: 43 residues processed: 258 average time/residue: 0.5125 time to fit residues: 223.6147 Evaluate side-chains 246 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 201 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 4.9990 chunk 192 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 251 optimal weight: 0.3980 chunk 139 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 233 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 50.0000 chunk 303 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 86 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 58472 Z= 0.148 Angle : 0.506 9.558 88261 Z= 0.257 Chirality : 0.029 0.227 11427 Planarity : 0.004 0.043 4167 Dihedral : 23.571 176.844 30992 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.17 % Allowed : 17.51 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.20), residues: 1660 helix: 0.40 (0.23), residues: 511 sheet: -0.10 (0.31), residues: 278 loop : -0.96 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 78 HIS 0.012 0.001 HIS R 82 PHE 0.015 0.001 PHE Y 26 TYR 0.010 0.001 TYR S 38 ARG 0.007 0.000 ARG T 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 226 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 49 GLN cc_start: 0.8544 (tt0) cc_final: 0.8237 (tt0) REVERT: E 78 TRP cc_start: 0.8636 (m100) cc_final: 0.7833 (m100) REVERT: K 106 GLU cc_start: 0.8696 (pp20) cc_final: 0.7827 (pp20) REVERT: K 113 MET cc_start: 0.8316 (mmt) cc_final: 0.8072 (mmt) REVERT: P 70 GLU cc_start: 0.7754 (mp0) cc_final: 0.7429 (mp0) REVERT: R 37 GLU cc_start: 0.8307 (pm20) cc_final: 0.7942 (pm20) REVERT: S 110 ARG cc_start: 0.8268 (tpp-160) cc_final: 0.7949 (tpp-160) REVERT: T 79 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8062 (p0) outliers start: 44 outliers final: 30 residues processed: 252 average time/residue: 0.5066 time to fit residues: 218.4702 Evaluate side-chains 242 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 211 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 30 TRP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 50 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 20.0000 chunk 304 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 198 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 338 optimal weight: 9.9990 chunk 281 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 112 optimal weight: 40.0000 chunk 177 optimal weight: 20.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 58472 Z= 0.411 Angle : 0.726 12.348 88261 Z= 0.362 Chirality : 0.038 0.239 11427 Planarity : 0.005 0.052 4167 Dihedral : 23.848 176.850 30992 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 5.19 % Allowed : 16.71 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1660 helix: -0.18 (0.22), residues: 512 sheet: -0.66 (0.31), residues: 277 loop : -1.21 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP T 80 HIS 0.016 0.002 HIS R 82 PHE 0.037 0.002 PHE Y 26 TYR 0.014 0.002 TYR S 38 ARG 0.017 0.001 ARG Y 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 198 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 128 ASN cc_start: 0.9427 (OUTLIER) cc_final: 0.9020 (m-40) REVERT: K 113 MET cc_start: 0.8406 (mmt) cc_final: 0.8193 (mmt) REVERT: R 34 GLU cc_start: 0.8964 (tt0) cc_final: 0.8754 (tt0) REVERT: S 110 ARG cc_start: 0.8403 (tpp-160) cc_final: 0.8074 (tpp-160) REVERT: T 12 ARG cc_start: 0.8755 (mmm160) cc_final: 0.8548 (mmm-85) REVERT: T 48 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: T 79 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8004 (p0) REVERT: 0 3 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.6078 (pt0) REVERT: 2 12 ARG cc_start: 0.8772 (tpp80) cc_final: 0.8460 (tpp-160) REVERT: 2 28 ARG cc_start: 0.8706 (mtt90) cc_final: 0.8282 (mtt90) REVERT: Z 26 LEU cc_start: 0.9038 (mm) cc_final: 0.8756 (mp) outliers start: 72 outliers final: 58 residues processed: 247 average time/residue: 0.5103 time to fit residues: 213.9492 Evaluate side-chains 254 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 192 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 30 TRP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 26 ASN Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain Z residue 37 ARG Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 5.9990 chunk 38 optimal weight: 40.0000 chunk 192 optimal weight: 7.9990 chunk 247 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 285 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 337 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 205 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 58472 Z= 0.209 Angle : 0.553 9.583 88261 Z= 0.281 Chirality : 0.032 0.225 11427 Planarity : 0.004 0.046 4167 Dihedral : 23.708 176.827 30992 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.82 % Allowed : 18.16 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1660 helix: 0.13 (0.23), residues: 511 sheet: -0.46 (0.31), residues: 272 loop : -1.12 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 78 HIS 0.005 0.001 HIS S 7 PHE 0.012 0.001 PHE Y 26 TYR 0.019 0.002 TYR J 125 ARG 0.006 0.000 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 209 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 TRP cc_start: 0.8774 (m100) cc_final: 0.7834 (m100) REVERT: L 95 LEU cc_start: 0.3940 (OUTLIER) cc_final: 0.3734 (pt) REVERT: R 37 GLU cc_start: 0.8367 (pm20) cc_final: 0.7948 (pm20) REVERT: T 12 ARG cc_start: 0.8718 (mmm160) cc_final: 0.8493 (mmm160) REVERT: T 79 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8032 (p0) REVERT: 0 27 LEU cc_start: 0.8909 (mm) cc_final: 0.8689 (mm) REVERT: 2 12 ARG cc_start: 0.8696 (tpp80) cc_final: 0.8402 (tpp-160) REVERT: 2 28 ARG cc_start: 0.8665 (mtt90) cc_final: 0.8196 (mtt90) outliers start: 53 outliers final: 45 residues processed: 244 average time/residue: 0.5114 time to fit residues: 212.9306 Evaluate side-chains 246 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 199 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 30 TRP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 39 ASP Chi-restraints excluded: chain Z residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 20.0000 chunk 134 optimal weight: 30.0000 chunk 201 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 214 optimal weight: 0.9980 chunk 229 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 265 optimal weight: 7.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 58472 Z= 0.378 Angle : 0.686 11.426 88261 Z= 0.344 Chirality : 0.037 0.257 11427 Planarity : 0.005 0.047 4167 Dihedral : 23.877 176.732 30992 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 4.61 % Allowed : 17.65 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.20), residues: 1660 helix: -0.19 (0.22), residues: 513 sheet: -0.64 (0.31), residues: 276 loop : -1.36 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 80 HIS 0.008 0.002 HIS S 7 PHE 0.014 0.002 PHE N 80 TYR 0.019 0.002 TYR J 125 ARG 0.008 0.001 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 200 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 118 MET cc_start: 0.8508 (mmt) cc_final: 0.7984 (mmm) REVERT: J 128 ASN cc_start: 0.9428 (OUTLIER) cc_final: 0.8999 (m-40) REVERT: L 95 LEU cc_start: 0.3805 (OUTLIER) cc_final: 0.3569 (pt) REVERT: R 34 GLU cc_start: 0.8970 (tt0) cc_final: 0.8747 (tt0) REVERT: T 12 ARG cc_start: 0.8802 (mmm160) cc_final: 0.8539 (mmm-85) REVERT: T 79 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.7998 (p0) REVERT: 0 3 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6081 (pt0) REVERT: 0 27 LEU cc_start: 0.8970 (mm) cc_final: 0.8763 (mm) REVERT: 2 12 ARG cc_start: 0.8814 (tpp80) cc_final: 0.8258 (tpt170) REVERT: 2 28 ARG cc_start: 0.8729 (mtt90) cc_final: 0.8292 (mtt90) REVERT: Z 26 LEU cc_start: 0.9021 (mm) cc_final: 0.8763 (mp) outliers start: 64 outliers final: 57 residues processed: 239 average time/residue: 0.5082 time to fit residues: 206.2808 Evaluate side-chains 255 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 194 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 128 ASN Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 30 TRP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 26 ASN Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 37 ARG Chi-restraints excluded: chain Z residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 7.9990 chunk 323 optimal weight: 6.9990 chunk 294 optimal weight: 10.0000 chunk 314 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 284 optimal weight: 0.8980 chunk 297 optimal weight: 0.0980 chunk 313 optimal weight: 1.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 58472 Z= 0.181 Angle : 0.537 11.238 88261 Z= 0.272 Chirality : 0.031 0.246 11427 Planarity : 0.004 0.045 4167 Dihedral : 23.716 176.681 30992 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.46 % Allowed : 19.09 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.20), residues: 1660 helix: 0.15 (0.23), residues: 511 sheet: -0.66 (0.31), residues: 277 loop : -1.18 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 78 HIS 0.005 0.001 HIS 2 16 PHE 0.011 0.001 PHE Y 26 TYR 0.022 0.002 TYR J 125 ARG 0.005 0.000 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 213 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 96 LYS cc_start: 0.2574 (mptt) cc_final: 0.1944 (mptt) REVERT: P 101 GLU cc_start: 0.7201 (pp20) cc_final: 0.6899 (pp20) REVERT: R 37 GLU cc_start: 0.8360 (pm20) cc_final: 0.8029 (pm20) REVERT: S 1 MET cc_start: 0.5006 (ptt) cc_final: 0.4757 (ptt) REVERT: T 48 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: T 79 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8028 (p0) REVERT: 0 3 GLN cc_start: 0.6406 (OUTLIER) cc_final: 0.5843 (pt0) REVERT: 2 12 ARG cc_start: 0.8768 (tpp80) cc_final: 0.8440 (tpp-160) REVERT: 2 28 ARG cc_start: 0.8686 (mtt90) cc_final: 0.8238 (mtt90) REVERT: Z 26 LEU cc_start: 0.8994 (mm) cc_final: 0.8722 (mp) REVERT: Z 54 VAL cc_start: 0.9107 (m) cc_final: 0.8875 (p) outliers start: 48 outliers final: 41 residues processed: 244 average time/residue: 0.5121 time to fit residues: 213.8158 Evaluate side-chains 248 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 204 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 30 TRP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 37 ARG Chi-restraints excluded: chain Z residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 7.9990 chunk 332 optimal weight: 1.9990 chunk 202 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 231 optimal weight: 0.6980 chunk 348 optimal weight: 2.9990 chunk 320 optimal weight: 5.9990 chunk 277 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 214 optimal weight: 0.6980 chunk 170 optimal weight: 20.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 58472 Z= 0.159 Angle : 0.504 10.784 88261 Z= 0.254 Chirality : 0.029 0.259 11427 Planarity : 0.004 0.044 4167 Dihedral : 23.546 176.420 30992 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.39 % Allowed : 19.31 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1660 helix: 0.33 (0.23), residues: 513 sheet: -0.56 (0.31), residues: 282 loop : -1.11 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 15 HIS 0.007 0.001 HIS 2 16 PHE 0.010 0.001 PHE S 75 TYR 0.020 0.002 TYR J 125 ARG 0.005 0.000 ARG Z 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 218 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 176 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7872 (p0) REVERT: P 101 GLU cc_start: 0.7218 (pp20) cc_final: 0.6904 (pp20) REVERT: R 37 GLU cc_start: 0.8359 (pm20) cc_final: 0.7963 (pm20) REVERT: T 48 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8035 (mp10) REVERT: T 79 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8153 (p0) REVERT: U 35 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8423 (p) REVERT: 0 3 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.5721 (pt0) REVERT: 2 12 ARG cc_start: 0.8944 (tpp80) cc_final: 0.8376 (tpt90) REVERT: 2 28 ARG cc_start: 0.8683 (mtt90) cc_final: 0.8242 (mtt90) REVERT: Z 54 VAL cc_start: 0.9047 (m) cc_final: 0.8831 (p) outliers start: 47 outliers final: 37 residues processed: 247 average time/residue: 0.5241 time to fit residues: 218.6131 Evaluate side-chains 250 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 208 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 30 TRP Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain Z residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 0.9990 chunk 295 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 256 optimal weight: 0.1980 chunk 40 optimal weight: 40.0000 chunk 77 optimal weight: 20.0000 chunk 278 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 285 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.075174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.053338 restraints weight = 305207.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.054632 restraints weight = 124909.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.055409 restraints weight = 82531.822| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 58472 Z= 0.195 Angle : 0.526 11.503 88261 Z= 0.264 Chirality : 0.030 0.260 11427 Planarity : 0.004 0.045 4167 Dihedral : 23.558 177.106 30992 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.46 % Allowed : 19.45 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1660 helix: 0.32 (0.23), residues: 513 sheet: -0.50 (0.31), residues: 280 loop : -1.13 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 78 HIS 0.005 0.001 HIS 2 16 PHE 0.019 0.001 PHE Y 26 TYR 0.022 0.001 TYR J 125 ARG 0.019 0.001 ARG Q 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5904.36 seconds wall clock time: 108 minutes 52.83 seconds (6532.83 seconds total)